Dark's graphics patch isn't just for the DeJap translation, it's for Star Ocean in general. It follows Nintendo's method of getting Street Fighter Alpha 2 working. It shouldn't break on Magno's translation, especially because Magno was in touch with Dark during development. I'll give it a go myself.
Edit: Having tested it, it looks like Magno has altered far too much. So while the graphics pack, designed for the Japanese ROM, works perfectly with DeJap's translation too, it looks like you're out of luck here.
Guessing Magno moved all the graphics pointers, which the DeJap one did not.
Edit2: Oh I see. Having read a Google Translate version of his page, I think I get the idea. Dark's patch works like Nintendo's SFA2 patch in that it uses the .sfrom format to "bypass" SDD-1 decompression. This is a feature of the .sfrom format that only SFA2 used, but worked fine with Star Ocean too. What Magno has done is make an all-in-one expanded ROM that includes the graphics. This is different from using .sfrom to bypass the SDD-1, and just like the big expanded DeJap translation out there, this won't work properly with the SNES Mini.
TLDR, his patch bakes the graphics into the ROM itself, but this is not how SDD-1 support on SNES Mini works.